[English] 日本語
Yorodumi
- PDB-5ic4: Crystal structure of caspase-3 DEVE peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ic4
TitleCrystal structure of caspase-3 DEVE peptide complex
Components
  • Caspase-3 subunit p12
  • Caspase-3 subunit p17
  • DEVE peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / apoptosis / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / response to amino acid / cell fate commitment / regulation of macroautophagy / response to tumor necrosis factor / Pyroptosis / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues ...Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeaman, J.E. / Julien, O. / Lee, P.S. / Rettenmaier, T.J. / Thomsen, N.D. / Wells, J.A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R21 CA186007 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM081051 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM097316 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA154802 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007175 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31 CA180378 United States
CitationJournal: Cell Death Differ. / Year: 2016
Title: Cacidases: caspases can cleave after aspartate, glutamate and phosphoserine residues.
Authors: Seaman, J.E. / Julien, O. / Lee, P.S. / Rettenmaier, T.J. / Thomsen, N.D. / Wells, J.A.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Caspase-3 subunit p17
D: Caspase-3 subunit p12
E: Caspase-3 subunit p17
F: Caspase-3 subunit p12
G: Caspase-3 subunit p17
H: Caspase-3 subunit p12
I: DEVE peptide
J: DEVE peptide
K: DEVE peptide
L: DEVE peptide


Theoretical massNumber of molelcules
Total (without water)131,39712
Polymers131,39712
Non-polymers00
Water95553
1
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Caspase-3 subunit p17
D: Caspase-3 subunit p12
I: DEVE peptide
J: DEVE peptide


Theoretical massNumber of molelcules
Total (without water)65,6986
Polymers65,6986
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-78 kcal/mol
Surface area17210 Å2
MethodPISA
2
E: Caspase-3 subunit p17
F: Caspase-3 subunit p12
G: Caspase-3 subunit p17
H: Caspase-3 subunit p12
K: DEVE peptide
L: DEVE peptide


Theoretical massNumber of molelcules
Total (without water)65,6986
Polymers65,6986
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-81 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.820, 177.796, 193.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

-
Components

#1: Protein
Caspase-3 subunit p17 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1


Mass: 19759.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein
Caspase-3 subunit p12 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1


Mass: 12601.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#3: Protein/peptide
DEVE peptide


Mass: 488.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% (v/v) tacsimate pH 7

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115859 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115859 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 33509 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dko

2dko


Resolution: 2.65→48.357 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1696 5.07 %
Rwork0.207 --
obs0.2086 33447 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→48.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7603 0 0 53 7656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027757
X-RAY DIFFRACTIONf_angle_d0.69610417
X-RAY DIFFRACTIONf_dihedral_angle_d13.212909
X-RAY DIFFRACTIONf_chiral_restr0.0281123
X-RAY DIFFRACTIONf_plane_restr0.0031331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.72790.3441540.33432587X-RAY DIFFRACTION98
2.7279-2.8160.33941440.33542597X-RAY DIFFRACTION100
2.816-2.91660.32281430.3092629X-RAY DIFFRACTION100
2.9166-3.03340.35211220.28712638X-RAY DIFFRACTION100
3.0334-3.17140.33621460.27442641X-RAY DIFFRACTION100
3.1714-3.33860.2821620.24782592X-RAY DIFFRACTION100
3.3386-3.54770.27611430.21292637X-RAY DIFFRACTION100
3.5477-3.82150.18681600.17372621X-RAY DIFFRACTION100
3.8215-4.20590.18931160.16882682X-RAY DIFFRACTION100
4.2059-4.8140.18271150.14422694X-RAY DIFFRACTION100
4.814-6.06320.18191520.17552671X-RAY DIFFRACTION100
6.0632-48.36550.19641390.17392762X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54670.3627-0.24661.9512-0.69012.13550.0937-0.01030.1604-0.1630.04810.1406-0.0241-0.2042-0.15120.3824-0.0029-0.02740.3973-0.00750.390423.2798-15.7593-11.8335
22.39640.4479-1.8561.1462-0.21633.64390.01980.0304-0.0888-0.19620.0707-0.08780.3323-0.012-0.06930.41870.0068-0.05410.3624-0.01920.383334.8541-23.5724-9.6764
31.7756-0.93620.13191.80690.14332.14560.0440.05390.08340.1160.0264-0.23610.0840.3778-0.09580.4401-0.0048-0.06760.4555-0.03620.456445.4154-19.598413.3407
41.379-0.9744-1.13341.77740.67532.88870.0719-0.0739-0.08930.09010.0169-0.00260.39440.0214-0.04940.4265-0.0278-0.07060.3690.00920.385131.6379-23.215311.3732
51.4283-0.6103-0.31222.2678-0.80621.83560.0762-0.0596-0.10350.14180.04610.32460.0338-0.1564-0.12920.4197-0.03130.0240.4020.00820.447557.2704-28.9378-36.3567
62.5765-0.43451.36541.484-1.12832.53170.0684-0.14040.0140.1839-0.0088-0.0831-0.26510.0673-0.05790.4207-0.06010.0530.4024-0.02840.399670.2027-22.8621-37.6209
71.64910.59120.39811.35290.22562.5657-0.04630.0281-0.2183-0.14990.0603-0.1470.17410.3031-0.0230.4135-0.02250.04480.43030.00050.475679.4781-26.1206-61.5575
81.57230.78680.8361.40170.32222.43450.03880.04840.0666-0.11230.00330.0725-0.26360.1558-0.03870.4077-0.02680.02770.37960.02430.405366.8773-20.5508-58.5489
96.2165-0.4398-0.67677.0490.4194.1448-0.03480.39360.9258-0.7069-0.13520.3767-0.79530.1780.21690.5845-0.0184-0.05810.45240.0660.526840.4888-13.2306-20.3382
104.4593-1.95583.08455.4295-2.76973.6486-0.51580.04590.01960.3602-0.5027-0.4447-0.65221.18660.80780.3762-0.1042-0.06390.51330.00460.619729.8512-11.700321.6648
114.5541-1.3925-1.84466.7717-0.8958.2966-0.5696-0.14730.00160.9575-0.39820.50660.36830.18330.8540.5484-0.0203-0.00050.46070.00360.618873.8615-34.9612-28.5768
124.90223.3567-4.11177.4759-0.8214.2176-0.52710.3997-0.4596-0.9777-0.3944-1.38780.2659-0.00570.79010.5603-0.0091-0.0630.65650.03760.702663.0865-30.3955-70.4859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more